Sedimentary nitrogen isotopic ratios are used as a proxy for ancient biogeochemical cycles on Earth's surface. It is generally accepted that sediment core tops record primary signatures because organic nitrogen (ON) is predominant in this part of the core. In contrast to such early to middle diagenetic stages, it is well known that heavier nitrogen isotope 15N tends to enrich the sedimentary and metamorphic rocks during latter diagenetic and metamorphic stages. However, there are some critical gaps in our understanding of nitrogen isotopic alteration associated with abiotic processes during early-middle diagenesis. In this study, we examined the isotope ratios of ammonium nitrogen in interstitial water (IW) and total nitrogen (TN), including exchangeable ammonium and mineral nitrogen, in the solid-phase of those associated organic-rich-sediment recovered by International Ocean Discovery Program (IODP) Expedition 385 cores drilled in the Guaymas Basin, Gulf of California, that contained ammonium-rich IW. The isotopic ratios (δ15N value) of TN were the most variable with depth compared to any other type of nitrogen. This variation can be interpreted as reflecting changes in the water mass environment in the basin caused by glacial–interglacial climate changes, which modifies the δ15N values of the marine primary producers. Thus, the δ15N value of TN is a proxy for environmental change in the basin, while each component of TN shows different trends. The δ15N values of IW and exchangeable ammonium did not exhibit significant changes with depth, but the latter values were about 3 ‰ enriched in 15N. This may be due to advective transport of solute into adjacent layers followed by the formation of an isotopic equilibrium between IW and exchangeable ammonium in the case of fast accumulation rate. The δ15N value of exchangeable ammonium was the highest among the other types of nitrogen with one exception, where the δ15N value of TN was the highest. The calculated δ15N values of ON based on mass balance were almost the same to those of associated TN in the shallow sediment layers (< 150 m below seafloor), but the difference in the δ15N values of TN and ON were significant in the deeper layers, where proportions of ON contents were <50%. In particular, in the layer where the δ15N value of TN was the highest, that of ON showed an even higher value and the difference reaches 3.5 ‰. The δ15N values of mineral nitrogen were similar to that of IW ammonium except the surface layers. Under such conditions, when δ15N value of TN is intermediate between those of mineral nitrogen and exchangeable ammonium, calculated δ15N value of ON is close to that of TN. On the other hand, if δ15N value of TN is out of the range between mineral nitrogen and exchangeable ammonium, it causes further difference in δ15N value of ON. It means that the fluctuation of δ15N values of TN is reduced relative to those of ON through depth. It has been considered that δ15N value of TN in sediment is similar to that of ON, and changes in the δ15N value of TN due to diagenesis are limited, but in such environment ON fluctuations over depth may be slightly underestimated.